Carlos -
I expect the problem is internal binary representation of the floating point
numbers. So the input trajectory file values may not be exactly
representable, though you are probably coming closer internally to your
input than it appears in your restart output (which also suffers from not
exactly representing the internal value). The only way to avoid this sort
of thing is with BCD - binary-coded decimal, which I believe is probably
available in Cobol and assembler :-) (probably PL/1 too).
Regards - Bob
----- Original Message -----
From: "Carlos Simmerling" <carlos.csb.sunysb.edu>
To: <amber-developers.scripps.edu>
Sent: Monday, February 05, 2007 5:18 PM
Subject: amber-developers: ptraj precision
>I am reading a trajectory file into ptraj and writing as restart, with no
>actions (no imaging, etc).
>
> I don't get quite what is in the traj file, does anyone know why?
> The precision error is enough to affect the energies
> and I want the actual coordinates from the traj file, not ones that are
> +/- 0.000005 etc.
> yes, I know that the ones in the traj file aren't exactly what was in the
> original MD, but the point is to do an exact
> conversion to restart.
> thanks
> carlos
>
> EXAMPLE
> input trajectory file:
> 18.438 29.157 33.019 18.614 28.133 32.690
> output restart from ptraj:
> 18.4379997 29.1569996 33.0190010 18.6140003 28.1329994 32.6899986
>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.stonybrook.edu
> Stony Brook, NY 11794-5115
> ===================================================================
>
>
>
>
Received on Wed Feb 07 2007 - 06:07:25 PST
